I had a similar situation - but I knew what's wrong. The boot rom is binary, debugging this is not easy. I wouldn't try it.
I'd check if the precondition for USB 1 to work are given.
1 - 12 Mhz crystal works:
Write a small test program, which switches to the external clock. Does this work?
2 - Check that USB works
Flash a USB example, where USB 1 is used. Does this work?
Most likely the answer here is no, you can now use the PC to see what's wrong.
- did the PC see the device being connected?
If no, something is wrong with the USB data connection, e.g. not connected.
- did the PC see the connection but didn't enumerate
Then the actual communication is broken.
In this case I'd check the power supplies.
Is the reference resistor connected?